CHANGELOG.md

RCSB Saguaro 3D Changelog

Semantic Versioning

[4.1.1] - 2024-08-26

Bug fix

• Multiple sequence alignment view color bug fixed

[4.1.0] - 2024-08-23

Improvements

• Ligand selection will always switch to the chain with most selected residues
• Ligand selection will not select other ligands

Dependency update

• rcsb-saguaro-app v6.2.5
• audit fix

[4.0.12] - 2024-08-20

Dependency update

• rcsb-saguaro-app v6.2.1

[4.0.11] - 2024-03-08

Improvement

• 1D3D checkboxes can use molstar info to display component availability. This is useful for non PDB entries

[4.0.10] - 2024-03-06

Improvement

• div delimiter increased width && transparent

Dependency update

• rcsb-saguaro-app v6.0.13
• rcsb-saguaro v3.0.7
• Multiple dependencies have been updated

[4.0.9] - 2024-01-10

Configuration

• Updated group views help link

[4.0.8] - 2024-01-10

Configuration

• Updated assembly view help link

Dependency update

• rcsb-saguaro-app v6.0.9
• dependencies audit fix

[4.0.7] - 2023-12-07

Dependency update

• rcsb-saguaro v3.0.7
• rcsb-saguaro-app v6.0.8

[4.0.6] - 2023-12-07

Dependency update

• rcsb-saguaro v3.0.6
• rcsb-saguaro-app v6.0.7

[4.0.5] - 2023-12-04

Improvement

• FocusResidueColorTheme used in assembly view

[4.0.4] - 2023-11-30

Dependency update

• rcsb-saguaro v3.0.5
• rcsb-saguaro-app v6.0.5

[4.0.3] - 2023-11-27

Dependency update

• rcsb-saguaro v3.0.4
• rcsb-saguaro-app v6.0.4

[4.0.2] - 2023-11-27

Dependency update

• rcsb-saguaro-app v6.0.3

[4.0.1] - 2023-11-27

Bug fix

• MSA polymer checkbox indicator bug fixed

[4.0.0] - 2023-11-22

Breaking changes

• Types are not anymore exposed from build/src
• All module classes and types are accessible from lib/
  • Modules format is ESNext
  • lib/commonjs exposes all modules in CommonJS format

Improvement

• MSA group displays Polymer/Ligand before loading the structure
  • Checkboxes are displayed in grey color

Code refactoring

• Sass @import changed to @use
• Styles sheets scss refactoring

Dependency update

• Multiple dependencies have been updated
• rcsb-saguaro-app v6.0.0
• rcsb-saguaro v3.0.0

[3.0.18] - 2023-10-03

Dependency update

• rcsb-saguaro-app v5.1.5
• @rcsb/rcsb-molstar v2.8.0,
• molstar v3.40.1

[3.0.17] - 2023-09-13

Bug fix

• rcsb-saguaro-app not updated

[3.0.16] - 2023-09-13

Dependency update

• rcsb-saguaro-app v5.1.4

[3.0.15] - 2023-09-08

Dependency update

• rcsb-saguaro-app v5.1.1
• @rcsb/rcsb-molstar v3.7.4
• Updated multiple dependencies

[3.0.14] - 2023-08-21

Bug fix

• Models were not superposed correctly in Alignment views

[3.0.13] - 2023-08-16

Improvements

• Non ball-and-stick representations for ligands will always include an additional ball-and-stick representation

Dependency update

• @rcsb/rcsb-molstar v3.7.3

[3.0.12] - 2023-08-10

Dependency update

• @rcsb/rcsb-molstar v3.7.2

[3.0.11] - 2023-08-10

Improvements

• New focus color theme to match the ribbon color in alignment views

Dependency update

• molstar v3.38.3

[3.0.10] - 2023-07-11

Bug fix

• Change sequence chain in Assembly view bug fixed

Dependency update

• rcsb-api-tools v4.1.13,
• rcsb-saguaro v2.5.13,
• rcsb-saguaro-app v5.0.8
• Updated multiple dependencies

[3.0.9] - 2023-05-19

Bug fix

• Chain checkbox label bug fixed in assembly view

[3.0.8] - 2023-05-19

Bug fix

• Chain checkbox display bug fixed in assembly view
• PFV onchange selection bug fixed in assembly view

[3.0.7] - 2023-05-16

Dependency update

• rcsb-saguaro-app v5.0.7

[3.0.6] - 2023-05-16

Configuration

• molstar and rcsb-molstar moved to peerDependencies

Dependency update

• rcsb-molstar v2.6.1
• molstar v3.35.0
• rcsb-saguaro-app v5.0.6

[3.0.5] - 2023-05-09

Dependency update

• rcsb-saguaro-app v5.0.5

[3.0.4] - 2023-05-03

Dependency update

• rcsb-saguaro-app v5.0.4

[3.0.3] - 2023-05-02

Dependency update

• rcsb-saguaro-app v5.0.3

[3.0.2] - 2023-05-02

Dependency update

• rcsb-saguaro-app v5.0.2

[3.0.1] - 2023-04-26

Style config

• Structure panel z-index removed and defined as molstar style

[3.0.0] - 2023-04-25

Improvements

• New entry method RcsbFv3DDataProviderInterface that ingests and displays external alignments
• New interface ComponentActionInterface used to define what actions are triggered after a new structure is loaded
• Interface LoadMolstarInterface<P,L> requires two generics: P load argument type and L load return type
• Interface ViewerModelMapManagerInterface<R,L> needs a new generic that defines the type returned by the loading method in LoadMolstarInterface.
  • It defines a new method getModelIdFromTrajectory(trajectory: L): string|undefined that is used to map loaded structure ids with user provided ids in LoadParams
• Custom View has been decoupled from RCSB view
• No StructureViewer data is passed to RcsbFvSequence all communication between panels is dne through the StateManager
• New RcsbViewBehaviourInterface interface to extend "1d" behaviour to events
• RcsbFv3DAbstract.render converted to async method
• Exposed molstar trajectory preset configuration
• Removed global state for MSA checkboxes

Dependency update

• rcsb-saguaro-app v5.0.0
• rcsb-saguaro v2.5.9
• rcsb-api-tools v4.1.3

Configuration

• All packages are transpiled and included in the final module

Breaking Changes

• rcsb-saguaro-app configuration RcsbFvAdditionalConfig.trackConfigModifier.alignment signature changed

[2.3.10] - 2023-03-03

Dependency update

• molstar update v3.31.2
• rcsb-molstar v2.5.11

[2.3.9] - 2023-03-02

Dependency update

• rcsb-saguaro-app v4.5.12

[2.3.8] - 2023-01-20

Dependency update

• rcsb-saguaro v2.5.8
• rcsb-saguaro-app v4.5.9

[2.3.7] - 2022-12-12

Bug fix

• assemblyId parameter has been removed from AlignmentTrajectoryPresetProvider
  • The provider check the first assembly that includes the entity

[2.3.6] - 2022-12-05

Display change

• MsaRowTitleCheckboxState are hide unless Mol* component exists

[2.3.5] - 2022-12-05

Improvement

• MsaPfvManagerFactory generalizes and replaces SequenceIdentityPfvManager and UniprotPfvManager
• MsaRowTitleCheckboxState is disabled if Mol* component is not generated
• MsaRowTitleComponent is blocked while structure is loaded

Dependency update

• rcsb-saguaro-app v4.5.7

[2.3.4] - 2022-11-28

Dependency update

• rcsb-saguaro-app v4.5.6
• rcsb-saguaro v2.5.5

[2.3.3] - 2022-11-23

Dependency update

• rcsb-saguaro-app v4.5.4

[2.3.2] - 2022-11-23

Dependency update

• rcsb-saguaro-app v4.5.3

[2.3.1] - 2022-11-23

New Features

• Sorting component MsaUiSortComponent for sequence identity MSA

Dependency update

• rcsb-saguaro-app v4.5.1
• rcsb-saguaro v2.5.4

[2.3.0] - 2022-11-08

Breaking Change

• Param LoadMethod.loadPdbIds has been removed. Multiple entries can be loaded passing a list of LoadMolstarInterface to RcsbFvStructureConfigInterface.loadConfig

Minor bug fixes

• CDN examples fixed

[2.2.1] - 2022-11-03

Improvement

• New attribute RcsbViewInterface.additionalContent to define the additionalContent React component

[2.2.0] - 2022-11-03

New Features

• New UniProt MSA 1D3D view
  • UniprotPfvManagerFactory builds UniProt Group MSA PFV
  • SequenceIdentityPfvManagerFactory builds Sequence Identity MSA PFV
  • MsaCallbackManagerFactory MSA 1D callbacks
  • MsaBehaviourObserver MSA 3D callbacks

[2.1.1] - 2022-10-17

Dependency update

• rcsb-saguaro-app v4.4.13
• rcsb-saguaro v2.2.16

Minor display update

• 1D PFV on-change resets 3D display

[2.1.0] - 2022-09-02

Major refactoring

• StructureViewerBehaviourObserverInterface factory of structure viewer behaviours
• StructureViewerBehaviourInterface abstraction of structure viewer callback events

[2.0.1] - 2022-09-01

Dependency update

• rcsb-saguaro-app v4.4.1
• rcsb-saguaro v2.2.7

[2.0.0] - 2022-08-31

Dependency update

• rcsb-saguaro-app v4.4.0
• rcsb-saguaro v2.2.6
• rcsb-api-tools v4.1.0
• rcsb-molstar v2.5.5
• molstar v3.13.0
• React v18
• Updated multiple dependencies

Major refactoring

• StructureViewerInterface abstraction to 3D structure viewer
  • ViewerCallbackManagerInterface defines 3D viewer callbacks
  • ViewerActionManagerInterface defines 3D viewer API
  • ViewerModelMapManagerInterface manager provides information of the loaded structures
• Global state interface RcsbFvStateInterface manages selections and loaded data

Breaking change

• FeatureViewInterface callback methods argument selectorManager: RcsbFvSelectorManager has been refactored to stateManager: RcsbFvStateManager

[1.4.4] - 2022-05-26

Dependency update

• rcsb-saguaro-app v4.3.6
• rcsb-api-tools v4.0.5

[1.4.3] - 2022-05-20

Dependency update

• rcsb-saguaro-app v4.3.5
• rcsb-api-tools v4.0.4

[1.4.2] - 2022-05-20

Dependency update

• rcsb-api-tools v4.0.3

[1.4.1] - 2022-05-05

Dependency update

• rcsb-saguaro-app v4.3.2

[1.4.0] - 2022-04-20

Improvement

• Extending 1D-3D display to any rcsb-saguaro-app PFV methods
  • PfvFactoryInterface defines how the PFV is created
  • CallbackManagerInterface defines the callbacks between the 1D and 3D panels
  • Current implementations: assembly and uniprot (partial implementation)

[1.3.10] - 2022-04-14

Dependency update

• rcsb-api-tools v4.0.1
• rcsb-saguaro-app v4.1.2

[1.3.9] - 2022-04-14

Dependency update

• rcsb-saguaro v2.0.6
• rcsb-saguaro-app v4.1.1

[1.3.8] - 2022-04-13

Dependency update

• rcsb-api-tools v4.0.0
• rcsb-saguaro v2.0.5
• rcsb-saguaro-app v4.1.0
• removed http-server module (3 high severity vulnerabilities)

[1.3.7] - 2022-04-07

Bug fixes

• assymId empty string bug fixed

[1.3.6] - 2022-04-07

Dependency update

• rcsb-saguaro update 2.0.4
• rcsb-saguaro-app update 4.0.7
• rcsb-api-tools update 3.0.2

[1.3.5] - 2022-03-28

Improvements

• RcsbFv3DAbstract.updateConfig method accepts partial states (Partial<RcsbFvStructureInterface> and Partial<RcsbFvSequenceInterface>)
• RcsbFv3DAbstract.unmount method includes an optional callback executed after when the component is unmounted
  • Assembly view Back link action has been refactored using the unmount-callback
• Minor code refactoring

[1.3.4] - 2022-03-07

Bug fixes

• NMR model change bug fix. New strategy to find the right modeId filtering the assemblyModelSate

[1.3.3] - 2022-03-07

Error publishing

• No changes, only examples were build

[1.3.2] - 2022-03-04

Configuration improvement

• RcsbFv3DAssemblyInterface configuration exposes a new optional parameterassemblyId to select the assembly that is being displayed

[1.3.1] - 2022-02-16

Dependency update

• Updated multiple dependencies

[1.3.0] - 2022-02-08

Improvements

• New class AssemblyModelSate to handle the assembly selection state in RcsbFvSequence.SequenceViews.AssemblyView.AssemblyView class
• New callback operatorChangeCallback function attached to operator dropdown menu changes

[1.2.1] - 2021-12-20

Dependency update

• Update to rcsb-api-tools 2.2.1

[1.2.0] - 2021-12-07

Improvements

• Support for assembly instance operators
• New selection interfaces SaguaroChain, SaguaroPosition, SaguaroRange and SaguaroSet
  • Support for selection involving multiple modelId
• rcsb-saguaro-app update 3.4.0
• rcsb-molstar update 2.0.0-dev.10

[1.1.0] - 2021-11-02

Minor configuration

• Exposed InstanceSequenceConfig for assembly view
• rcsb-saguaro-app update 3.2.1

[1.0.1] - 2021-11-02

Dependency update

• rcsb-saguaro-app update 3.1.1

[1.0.0] - 2021-10-27

General

• Initial release