TmMolStar

rcsb-saguaro-3D

RCSB Saguaro Web 3D is an open-source library built on the top of the RCSB Saguaro 1D Feature Viewer and RCSB Molstar designed to display protein features at the RCSB Web Site. The package collects protein annotations from the 1D Coordinate Server and the main RCSB Data API and generates Protein Feature Summaries. The package allows access to RCSB Saguaro and Molstar methods to add or change the displayed data. <!---

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CDN JavaScript

<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-3d@1.0.0/build/dist/app.js" type="text/javascript"></script>

Node Module Instalation

npm install @rcsb/rcsb-saguaro-3d

Building & Running

Build app

npm install
npm run buildApp

Build examples

npm run buildExamples

From the root of the project:

http-server -p PORT-NUMBER

and navigate to localhost:PORT-NUMBER/build/examples/

Library Documentation

TypeScript full classes documentation can be found here.

Main Classes and Interfaces

Assembly view

Class RcsbFv3DAssembly (src/RcsbFv3D/RcsbFv3DAssembly.tsx) builds a predefined 1D/3D view for PDB entries. This method is used in the RCSB PDB web portal to display 1D features on PDB entries (ex: 4hhb). Its configuration requires a single PDB ID. In addition, additionalConfig allows to configure the feature viewer as describe in rcsb-saguaro-app [API]("https://rcsb.github.io/rcsb-saguaro-app/interfaces/rcsbfvadditionalconfig.html"). This parameter exposes the board configuration through the attribute boardConfig ([ref]("https://rcsb.github.io/rcsb-saguaro/interfaces/rcsbfvboardconfiginterface.html")).

interface RcsbFv3DAssemblyInterface extends RcsbFv3DAbstractInterface {
   config: {
        entryId: string;
        title?: string;
        subtitle?: string;
    };
    additionalConfig?: RcsbFvAdditionalConfig;
}

Source code example can be found in src/examples/assembly/index.ts.

Custom view

Class RcsbFv3DCustom file src/RcsbFv3D/RcsbFv3DCustom.tsx builds a customized view between one or more feature viewers and a single Molstar plugin. The configuration interface encodes the parameters needed for the feature viewers (sequencePanelConfig) and the molstar plugin (structurePanelConfig).

interface RcsbFv3DCustomInterface extends RcsbFv3DAbstractInterface {
    structurePanelConfig: RcsbFvStructureInterface;
    sequencePanelConfig: {
        config: CustomViewInterface;
        title?: string;
        subtitle?: string;
    };
}

Information in the sequence panels is organized in blocks where each block contains the parameter (blockConfig) to display one or more feature viewers. The optional parameter blockSelectorElement defines a React component that renders the html element used to change the displayed block. The class BlockSelectorManager is used to select which block is displayed. For example, blockSelectorManager.setActiveBlock("myBlock") will display the feature viewers defined in the block with blockId "myBlock" (see FeatureBlockInterface). Additionally, blockChangeCallback defines a function that will be executed when the displayed block changes.

interface CustomViewInterface {
    blockConfig: FeatureBlockInterface | Array<FeatureBlockInterface>;
    blockSelectorElement?: (blockSelector: BlockSelectorManager) => JSX.Element;
    blockChangeCallback?: (plugin: SaguaroPluginPublicInterface, pfvList: Array<RcsbFv>, selection: RcsbFvSelectorManager) => void;
}

Source code example can be found in src/examples/multiple-chain/index.ts.

Each block must contain a unique block identifier (blockId) and the configuration for all the feature viewers that will be rendered when the block is activated (featureViewConfig).

interface FeatureBlockInterface {
    blockId:string;
    featureViewConfig: Array<FeatureViewInterface> | FeatureViewInterface;
}

The interface fo each feature viewer defines its dynamic interaction with the molstar plugin through different event callbacks

• sequenceSelectionChangeCallback defines how the molstar plugin reacts when the feature viewer selection changes
• sequenceElementClickCallback defines how the molstar plugin reacts when a feature viewer element (positional annotation) is clicked
• sequenceHoverCallback defines how the molstar plugin reacts when the mouse hovers the feature viewer or any element
• structureSelectionCallback defines how the protein feature viewer reacts when the molstar plugin selection changes
• structureHoverCallback defines how the protein feature viewer reacts when displayed models on the molstar plugin are hovered

export interface FeatureViewInterface {
    boardId?:string;
    boardConfig: RcsbFvBoardConfigInterface;
    rowConfig: Array<RcsbFvRowConfigInterface>;
    sequenceSelectionChangeCallback: (plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => void;
    sequenceElementClickCallback: (plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, d: RcsbFvTrackDataElementInterface) => void;
    sequenceHoverCallback: (plugin: SaguaroPluginPublicInterface, selectorManager: RcsbFvSelectorManager, hoverRegion: Array<RcsbFvTrackDataElementInterface>) => void;
    structureSelectionCallback: (plugin: SaguaroPluginPublicInterface, pfv: RcsbFv, selectorManager: RcsbFvSelectorManager) => void;
    structureHoverCallback: (plugin: SaguaroPluginPublicInterface, pfv: RcsbFv, selectorManager: RcsbFvSelectorManager) => void;
}

plugin: SaguaroPluginPublicInterface exposes the interface to interact with the molstar plugin and change model representations ([ref]("https://rcsb.github.io/rcsb-saguaro-3d/interfaces/saguaropluginpublicinterface.html")). It provides multiple methods such as hide, display or select to modify how structural data is displayed. The parameter pfv: RcsbFv allows to access the feature viewer API ([ref]("https://rcsb.github.io/rcsb-saguaro/classes/rcsbfv.html")). It exposes methods to modify selections, change board configuration, zoom or adding new tracks.

Source code example can be found in src/examples/single-chain/index.tsx

Contributing

All contributions are welcome. Please, make a pull request or open an issue.

License

The MIT License

Copyright (c) 2021 - now, RCSB PDB and contributors

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.