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Segura Mora","email":"joan.segura@rcsb.org"},"license":"MIT","homepage":"https://rcsb.github.io/rcsb-saguaro-3d","keywords":["3D","structure","1D","viewer","sequence","annotations","gene","protein","PDB","RCSB","UniProt"],"repository":{"url":"git://github.com/rcsb/rcsb-saguaro-3d.git","type":"git"},"description":"RCSB Molstar/Saguaro Web App","maintainers":[{"email":"jsegurmor@gmail.com","name":"bioinsilico"},{"email":"yana.v.rose@gmail.com","name":"yana.rose"},{"email":"charmi.bhikadiya@rcsb.org","name":"charmi.bhikadiya"},{"email":"ronald.brown@rcsb.org","name":"ronald-brown"},{"email":"maria.voigt@rcsb.org","name":"mariavoigt"},{"email":"jonstargaryen90@gmail.com","name":"sebastian.bittrich"}],"readme":"# rcsb-saguaro-3D\n\nRCSB Saguaro Web 3D is an open-source library built on the top of the [RCSB Saguaro 1D Feature Viewer](https://rcsb.github.io/rcsb-saguaro)\nand [RCSB Molstar](https://github.com/rcsb/rcsb-Molstar) designed to display protein features at the [RCSB Web Site](https://www.rcsb.org). \nThe package collects protein annotations from the [1D Coordinate Server](https://1d-coordinates.rcsb.org) \nand the main [RCSB Data API](https://data.rcsb.org) and generates Protein Feature Summaries. \nThe package allows access to RCSB Saguaro and Molstar methods to add or change the displayed data. \n\nWhen using rcsb-saguaro, please cite:\n\nJoan Segura, Yana Rose, Sebastian Bittrich, Stephen K Burley, Jose M Duarte.\nRCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies, Bioinformatics, 2022; https://doi.org/10.1093/bioinformatics/btac317\n\n<!---\n<div id=\"pfv\"></div>\n<script crossorigin src=\"https://unpkg.com/react@19/cjs/react.production.js\"></script>\n<script crossorigin src=\"https://unpkg.com/react-dom@19/cjs/react-dom.production.js\"></script>\n<script crossorigin src=\"https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-3d/build/app.js\"></script>\n<script type=\"text/javascript\">\nvar __assign = (this && this.__assign) || function () {\n    __assign = Object.assign || function(t) {\n        for (var s, i = 1, n = arguments.length; i < n; i++) {\n            s = arguments[i];\n            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))\n                t[p] = s[p];\n        }\n        return t;\n    };\n    return __assign.apply(this, arguments);\n};\nvar rowConfigChainA = [\n    {\n        trackId: \"sequenceTrack\",\n        trackHeight: 20,\n        trackColor: \"#F9F9F9\",\n        displayType: \"sequence\" /* SEQUENCE */,\n        nonEmptyDisplay: true,\n        rowTitle: \"CHAIN A\",\n        trackData: [\n            {\n                begin: 1,\n                value: \"CGVPAIQPVLSGLSRIVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN\"\n            }\n        ]\n    }, {\n        trackId: \"blockTrack\",\n        trackHeight: 20,\n        trackColor: \"#F9F9F9\",\n        displayType: \"block\" /* BLOCK */,\n        displayColor: \"#76ae91\",\n        rowTitle: \"FEATURE\",\n        trackData: [{\n            begin: 20,\n            end: 25\n        }, {\n            begin: 150,\n            end: 160\n        }]\n    }\n];\nvar rowConfigChainB = [\n    {\n        trackId: \"sequenceTrack\",\n        trackHeight: 20,\n        trackColor: \"#F9F9F9\",\n        displayType: \"sequence\" /* SEQUENCE */,\n        nonEmptyDisplay: true,\n        rowTitle: \"CHAIN B\",\n        trackData: [\n            {\n                begin: 1,\n                value: \"TEFGSELKSFPEVVGKTVDQAREYFTLHYPQYDVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG\"\n            }\n        ]\n    }, {\n        trackId: \"blockTrack\",\n        trackHeight: 20,\n        trackColor: \"#F9F9F9\",\n        displayType: \"block\" /* BLOCK */,\n        displayColor: \"#f17070\",\n        rowTitle: \"FEATURE\",\n        trackData: [{\n            begin: 20,\n            end: 50\n        }]\n    }\n];\nvar fvConfigChainA = {\n    boardId: \"1acb.A_board\",\n    boardConfig: {\n        range: {\n            min: 1,\n            max: 245\n        },\n        disableMenu:true,\n        rowTitleWidth: 80,\n        trackWidth: 670,\n        includeAxis: true\n    },\n    rowConfig: rowConfigChainA,\n    sequenceSelectionChangeCallback: function (plugin, stateManager, sequenceRegion) {\n        stateManager.selectionState.clearSelection(\"select\", { modelId: \"1acb_board\", labelAsymId: \"A\" });\n        plugin.clearSelection(\"select\", { modelId: \"1acb_board\", labelAsymId: \"A\" });\n        if (sequenceRegion.length > 0) {\n            var regions = sequenceRegion.map(function (r) {\n                var _a;\n                return ({\n                    modelId: \"1acb_board\",\n                    labelAsymId: \"A\",\n                    region: { begin: r.begin, end: (_a = r.end) !== null && _a !== void 0 ? _a : r.begin, source: \"sequence\" }\n                });\n            });\n            stateManager.selectionState.addSelectionFromMultipleRegions(regions, \"select\");\n            plugin.select(regions.map(function (r) { return (__assign(__assign({}, r), { begin: r.region.begin, end: r.region.end })); }), \"select\", \"add\");\n        }\n        else {\n            plugin.resetCamera();\n        }\n    },\n    sequenceElementClickCallback: function (plugin, selectorManager, d) {\n        var _a;\n        if (d != null)\n            plugin.cameraFocus(\"1acb_board\", \"A\", d.begin, (_a = d.end) !== null && _a !== void 0 ? _a : d.begin);\n    },\n    sequenceHoverCallback: function (plugin, selectorManager, elements) {\n        if (elements == null || elements.length == 0)\n            plugin.clearSelection(\"hover\");\n        else\n            plugin.select(elements.map(function (e) {\n                var _a;\n                return ({\n                    modelId: \"1acb_board\",\n                    labelAsymId: \"A\",\n                    begin: e.begin,\n                    end: (_a = e.end) !== null && _a !== void 0 ? _a : e.begin\n                });\n            }), \"hover\", \"set\");\n    },\n    structureSelectionCallback: function (plugin, pfv, stateManager) {\n        const sel = stateManager.selectionState.getSelectionWithCondition(\"1acb_board\", \"A\", \"select\");\n        if(sel == null) {\n            pfv.clearSelection(\"select\");\n            plugin.resetCamera();\n        }else {\n            pfv.setSelection({elements: sel.regions, mode: \"select\"});\n        }\n    },\n    structureHoverCallback: function (plugin, pfv, stateManager) {\n        var sel = stateManager.selectionState.getSelectionWithCondition(\"1acb_board\", \"A\", \"hover\");\n        if (sel == null)\n            pfv.clearSelection(\"hover\");\n        else\n            pfv.setSelection({ elements: sel.regions, mode: \"hover\" });\n    }\n};\nvar fvConfigChainB = {\n    boardId: \"1acb.B_board\",\n    boardConfig: {\n        range: {\n            min: 1,\n            max: 70\n        },\n        disableMenu:true,\n        rowTitleWidth: 80,\n        trackWidth: 670,\n        includeAxis: true\n    },\n    rowConfig: rowConfigChainB,\n    sequenceSelectionChangeCallback: function (plugin, stateManager, sequenceRegion) {\n        stateManager.selectionState.clearSelection(\"select\", { modelId: \"1acb_board\", labelAsymId: \"B\" });\n        plugin.clearSelection(\"select\", { modelId: \"1acb_board\", labelAsymId: \"B\" });\n        if (sequenceRegion.length > 0) {\n            var regions = sequenceRegion.map(function (r) {\n                var _a;\n                return ({\n                    modelId: \"1acb_board\",\n                    labelAsymId: \"B\",\n                    region: { begin: r.begin, end: (_a = r.end) !== null && _a !== void 0 ? _a : r.begin, source: \"sequence\" }\n                });\n            });\n            stateManager.selectionState.addSelectionFromMultipleRegions(regions, \"select\");\n            plugin.select(regions.map(function (r) { return (__assign(__assign({}, r), { begin: r.region.begin, end: r.region.end })); }), \"select\", \"add\");\n        }\n        else {\n            plugin.resetCamera();\n        }\n    },\n    sequenceElementClickCallback: function (plugin, selectorManager, d) {\n        var _a;\n        if (d != null)\n            plugin.cameraFocus(\"1acb_board\", \"B\", d.begin, (_a = d.end) !== null && _a !== void 0 ? _a : d.begin);\n    },\n    sequenceHoverCallback: function (plugin, selectorManager, elements) {\n        if (elements == null || elements.length == 0)\n            plugin.clearSelection(\"hover\");\n        else\n            plugin.select(elements.map(function (e) {\n                var _a;\n                return ({\n                    modelId: \"1acb_board\",\n                    labelAsymId: \"B\",\n                    begin: e.begin,\n                    end: (_a = e.end) !== null && _a !== void 0 ? _a : e.begin\n                });\n            }), \"hover\", \"set\");\n    },\n    structureSelectionCallback: function (plugin, pfv, stateManager) {\n        const sel = stateManager.selectionState.getSelectionWithCondition(\"1acb_board\", \"B\", \"select\");\n        if (sel == null) {\n            pfv.clearSelection(\"select\");\n            plugin.resetCamera();\n        }\n        else {\n            pfv.setSelection({ elements: sel.regions, mode: \"select\" });\n        }\n    },\n    structureHoverCallback: function (plugin, pfv, stateManager) {\n        var sel = stateManager.selectionState.getSelectionWithCondition(\"1acb_board\", \"B\", \"hover\");\n        if (sel == null)\n            pfv.clearSelection(\"hover\");\n        else\n            pfv.setSelection({ elements: sel.regions, mode: \"hover\" });\n    }\n};\nvar blockChainA = {\n    blockId: \"chainA\",\n    featureViewConfig: [fvConfigChainA]\n};\nvar blockChainB = {\n    blockId: \"chainB\",\n    featureViewConfig: [fvConfigChainB]\n};\nvar blockSelectorElement = function (blockSelectorManager) {\n    return (React.createElement(\"div\", null,\n        React.createElement(\"select\", { onChange: function (e) {\n                    blockSelectorManager.setActiveBlock(e.target.value);\n                } },\n            React.createElement(\"option\", { value: \"chainA\" }, \"Chain A\"),\n            React.createElement(\"option\", { value: \"chainB\" }, \"Chain B\"))));\n};\nvar customConfig = {\n    blockConfig: [blockChainA, blockChainB],\n    blockSelectorElement: blockSelectorElement\n};\nvar sequenceConfig = {\n    title: undefined,\n    subtitle: undefined,\n    config: customConfig\n};\nvar molstarConfig = {\n    loadConfig: {\n        loadMethod: \"loadPdbId\",\n        loadParams: {\n            entryId: \"1acb\",\n            id: \"1acb_board\"\n        }\n    },\n    structureViewerConfig: {\n        viewerProps:{\n            showImportControls: true,\n            showSessionControls: false\n        }\n    },\n};\ndocument.addEventListener(\"DOMContentLoaded\", function (event) {\n    var panel3d = new RcsbFv3D.custom({\n        elementId: \"pfv\",\n        structurePanelConfig: molstarConfig,\n        sequencePanelConfig: sequenceConfig,\n        cssConfig: {\n            overwriteCss:true,\n            rootPanel:{\n                display:\"flex\",\n                flexDirection:\"column-reverse\"\n            },\n            structurePanel:{\n                width: 750,\n                height: 700\n            },\n            sequencePanel:{\n                width:750,\n                marginBottom:5\n            }\n        },\n    });\n    panel3d.render();\n});\n</script>\n--->\n### CDN JavaScript\n`<script src=\"https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-3d@4.0.0/build/app.min.js\" type=\"text/javascript\"></script>`\n\n### Node Module Instalation\n`npm install @rcsb/rcsb-saguaro-3d`\n\n## Building & Running\n\n### Build app\n    npm install\n    npm run buildApp\n\n### Testing\nDifferent testing example are available in the `src/examples` folder\n- `npm install`\n- `npm run devServer`\n\nGo to:\n\n- `http://localhost:9000/assembly.html`\n- `http://localhost:9000/assembly-interface.html`\n- `http://localhost:9000/uniprot.html`\n...\n\n### Library Documentation\n- TypeScript classes and documentation can be found [here](https://rcsb.github.io/rcsb-saguaro-3d/index.html)\n\n### Main Classes and Interfaces\n\n#### Assembly view\nClass **`RcsbFv3DAssembly`** (`src/RcsbFv3D/RcsbFv3DAssembly.tsx`) builds a predefined 1D/3D view for PDB assemblies. This method is used in the RCSB PDB web portal \nto display 1D positional features of PDB models (ex: [4hhb](https://www.rcsb.org/3d-sequence/4HHB)). Its configuration requires a single PDB Id. \nIn addition, `additionalConfig` allows to configure the feature viewer as describe in rcsb-saguaro-app [API](https://rcsb.github.io/rcsb-saguaro-app/).\nThis parameter exposes the board configuration through the attribute `boardConfig` ([ref](https://rcsb.github.io/rcsb-saguaro/interfaces/RcsbFvBoardConfigInterface.html)).\nThe component will be mounted in the html element with id `elementId`. If there is no html element in the current document,\na new div element will be added, and the component will be displayed in full screen mode. \n\n```typescript\nexport interface RcsbFv3DAssemblyInterface {\n    elementId?: string;\n    config: {\n        entryId: string;\n        assemblyId?: string;\n        title?: string;\n        subtitle?: string;\n    };\n    additionalConfig?: RcsbFv3DAssemblyAdditionalConfig;\n    instanceSequenceConfig?: InstanceSequenceConfig;\n    molstarProps?: Partial<ViewerProps>;\n    cssConfig?: RcsbFv3DCssConfig;\n}\n```\nSource code example can be found in `src/examples/assembly/index.tsx`.\n#### Custom view\n\nClass **`RcsbFv3DCustom`** file `src/RcsbFv3D/RcsbFv3DCustom.tsx` builds a customized view between one or more feature viewers and a single Molstar plugin.\nThe configuration interface encodes the parameters for the feature viewers (`sequencePanelConfig`), the Molstar plugin (`structurePanelConfig`) and \ntheir dynamic interaction.\n\n```typescript\ninterface RcsbFv3DCustomInterface  {\n    elementId?: string;\n    structurePanelConfig: RcsbFvStructureConfigInterface<\n        LoadMolstarInterface,\n        { viewerProps:Partial<ViewerProps> }\n    >;\n    sequencePanelConfig: {\n        config: CustomViewInterface<LoadMolstarInterface>;\n        title?: string;\n        subtitle?: string;\n    }\n    cssConfig?: RcsbFv3DCssConfig;\n\n}\n```\n\n![Alt text](https://raw.githubusercontent.com/rcsb/rcsb-saguaro-3d/master/.github/img/config_img.png \"Custom config schema\")\n\n##### Structural Panel\n\nThe structural panel configuration `structurePanelConfig: RcsbFvStructureConfigInterface<LoadMolstarInterface,{viewerProps:Partial<ViewerProps>}>` includes the loading configuration for the 3D structural data\nand the Molstar plugin. A full description of the structural panel configuration can be found [here](https://rcsb.github.io/rcsb-saguaro-3d/interfaces/RcsbFvStructure_RcsbFvStructure.RcsbFvStructureConfigInterface.html)\n\n```typescript\ninterface RcsbFvStructureConfigInterface<R,S> {\n    loadConfig: R | Array<R>;\n    structureViewerConfig: S;\n}\n```\n\nThe attribute `loadConfig: LoadMolstarInterface` encodes the configuration for loading the 3D structural data. \n \n```typescript\ninterface LoadMolstarInterface {\n    loadMethod: LoadMethod;\n    loadParams: LoadParams;\n}\n```\n- `loadMethod: LoadMethod`  is an enumerated value  that indicates the source of the structural models\n```typescript\nenum LoadMethod {\n    loadPdbId = \"loadPdbId\",\n    loadStructureFromUrl = \"loadStructureFromUrl\"\n}\n```\n- `loadParams: LoadParams` encode the parameters needed to collect and load the data. If `id` is provided, it can be used to identify the 3D models\nin the methods defined by `SaguaroPluginPublicInterface`\n\n```typescript\ninterface LoadParams {\n    id?: string;\n    pdbId?: string;\n    url?: string,\n    isBinary?: boolean\n}\n```\n\n##### Sequence panel\n\nThe sequence panel organizes information in different blocks where each block encodes the configuration \n(`blockConfig`) to display one or more feature viewers. Only a single block can be displayed at a time. The optional parameter `blockSelectorElement` defines a React component \nthat renders the html element used to change the displayed block. The class `BlockSelectorManager` is used to select which block is \ndisplayed are those that are hidden. For example, `blockSelectorManager.setActiveBlock(\"myBlock\")` will display the feature viewers defined in the block \nwith `blockId` `\"myBlock\"` (see `FeatureBlockInterface`) and hide the others. Additionally, `blockChangeCallback` defines a function that will be executed \nwhen the displayed block changes.\n\n```typescript\ninterface CustomViewInterface {\n    blockConfig: FeatureBlockInterface | Array<FeatureBlockInterface>;\n    blockSelectorElement?: (blockSelector: BlockSelectorManager) => JSX.Element;\n    blockChangeCallback?: (plugin: StructureViewerPublicInterface, pfvList: Array<RcsbFv>, selection: RcsbFvSelectorManager) => void;\n}\n``` \n\nSource code example can be found in `src/examples/multiple-chain/index.tsx`.\n\nEach block must contain a unique block identifier (`blockId`) and the configuration for all the feature viewers that will be rendered\nwhen the block is activated (`featureViewConfig`).\n```typescript\ninterface FeatureBlockInterface {\n    blockId:string;\n    featureViewConfig: Array<FeatureViewInterface> | FeatureViewInterface;\n}\n```\n\nThe interface for each feature viewer defines its dynamic interaction with the Molstar plugin through different event callbacks functions\n\n- `sequenceSelectionChangeCallback` defines how the Molstar plugin reacts when the feature viewer selection changes\n- `sequenceElementClickCallback` defines how the Molstar plugin reacts when a feature viewer element (positional annotation) is clicked\n- `sequenceHoverCallback` defines how the Molstar plugin reacts when the mouse hovers the feature viewer or any of its elements\n- `structureSelectionCallback` defines how the protein feature viewer reacts when the Molstar plugin selection changes\n- `structureHoverCallback` defines how the protein feature viewer reacts when displayed models on the Molstar plugin are hovered\n\n```typescript\nexport interface FeatureViewInterface {\n    boardId?:string;\n    boardConfig: RcsbFvBoardConfigInterface;\n    rowConfig: Array<RcsbFvRowConfigInterface>;\n    sequenceSelectionChangeCallback: (plugin: StructureViewerPublicInterface, selectorManager: RcsbFvSelectorManager, sequenceRegion: Array<RcsbFvTrackDataElementInterface>) => void;\n    sequenceElementClickCallback: (plugin: StructureViewerPublicInterface, selectorManager: RcsbFvSelectorManager, d: RcsbFvTrackDataElementInterface) => void;\n    sequenceHoverCallback: (plugin: StructureViewerPublicInterface, selectorManager: RcsbFvSelectorManager, hoverRegion: Array<RcsbFvTrackDataElementInterface>) => void;\n    structureSelectionCallback: (plugin: StructureViewerPublicInterface, pfv: RcsbFv, selectorManager: RcsbFvSelectorManager) => void;\n    structureHoverCallback: (plugin: StructureViewerPublicInterface, pfv: RcsbFv, selectorManager: RcsbFvSelectorManager) => void;\n}\n```\n\n`plugin: SaguaroPluginPublicInterface` exposes the interface to interact with the Molstar plugin\nand change model representations ([ref](https://rcsb.github.io/rcsb-saguaro-3d/interfaces/RcsbFv3DAssembly._internal_.StructureViewerPublicInterface.html)). \nIt provides multiple methods such as hide, display or select to modify how structural data is displayed. The parameter `pfv: RcsbFv` \nallows to access the feature viewer API ([ref](https://rcsb.github.io/rcsb-saguaro/classes/RcsbFv.html)). It exposes methods to modify \nselections, change board configuration, zoom or adding new tracks.\n \nSource code example can be found in `src/examples/single-chain/index.tsx`\n\nContributing\n---\nAll contributions are welcome. Please, make a pull request or open an issue.\n\nLicense\n---\n\nThe MIT License\n\n    Copyright (c) 2021 - now, RCSB PDB and contributors\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.","readmeFilename":"README.md"}