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  1. index.html +276 -16
index.html CHANGED
@@ -1,19 +1,279 @@
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  <!DOCTYPE html>
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  <html>
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- <head>
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- <meta charset="utf-8" />
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- <meta name="viewport" content="width=device-width" />
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- <title>My static Space</title>
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- <link rel="stylesheet" href="style.css" />
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- </head>
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- <body>
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- <div class="card">
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- <h1>Welcome to your static Space!</h1>
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- <p>You can modify this app directly by editing <i>index.html</i> in the Files and versions tab.</p>
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- <p>
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- Also don't forget to check the
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- <a href="https://huggingface.co/docs/hub/spaces" target="_blank">Spaces documentation</a>.
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- </p>
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- </div>
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- </body>
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  </html>
 
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  <!DOCTYPE html>
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  <html>
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+
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+ <head>
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+
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+ <link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.2/fonts.css" type="text/css" media="all"/>
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+ <script src="https://d3js.org/d3.v4.min.js" charset="utf-8"></script>
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+ <script type="text/javascript" src="https://www.ebi.ac.uk/pdbe/pdb-component-library/js/protvista-pdb-3.3.0.js"></script>
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+
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+ </head>
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+
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+ <body>
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+ <h4>ProtVista PDB custom data demo</h4>
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+
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+ <div>
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+ <protvista-pdb custom-data="true" id="pv1"></protvista-pdb>
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+ </div>
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+
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+ <script>
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+ document.addEventListener('DOMContentLoaded', () => {
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+
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+ //Get web-component element
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+ const pvInstance = document.getElementById('pv1');
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+ if(!pvInstance) return;
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+ (async () => {
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+
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+ // PDBe sequence conservation api data
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+ let scFetch = await fetch('https://www.ebi.ac.uk/pdbe/graph-api/uniprot/sequence_conservation/P29373');
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+ let scResponseData = await scFetch.json();
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+ const seqConservationData = scResponseData;
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+ // seqConservationData is a json array with following fields. Please refer the fetch api url for the data struture
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+ // [
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+ // {
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+ // "start": 1,
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+ // "end": 1,
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+ // "conservation_score": 1,
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+ // "tooltipContent": "Conservation score: 1",
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+ // "amino": [
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+ // {
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+ // "end": 1,
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+ // "letter": "P",
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+ // "proba": 0.428,
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+ // "start": 1,
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+ // "color": "#c0c000",
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+ // "tooltipContent": "Amino acid: PRO<br/>Probability: 42.80%"
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+ // },...
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+ // ]
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+ // }...
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+ // ]
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+
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+ // PDBe variation api data
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+ let vrFetch = await fetch('https://www.ebi.ac.uk/pdbe/graph-api/uniprot/protvista/variation/P29373');
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+ let vrResponseData = await vrFetch.json();
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+ const variationData = vrResponseData;
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+ // variationData is a json with following fields. Please refer the fetch api url for the data struture
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+ // {
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+ // "sequence": "PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE",
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+ // "variants": [
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+ // {
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+ // "accession": "NC_000001.11:g.156705439T>C",
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+ // "association": [],
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+ // "clinicalSignificances": null,
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+ // "color": "#002594",
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+ // "end": "2",
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+ // "polyphenScore": 0.003,
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+ // "siftScore": 0.055,
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+ // "sourceType": "large_scale_study",
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+ // "start": "2",
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+ // "tooltipContent": "XYZ Variant",
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+ // "variant": "S",
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+ // "xrefNames": [
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+ // "gnomAD"
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+ // ],
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+ // "keywords": [ // Keywords are used to filter the variats
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+ // "predicted",
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+ // "large_scale_studies"
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+ // ]
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+ // },...
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+ // ]
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+ // }
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+
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+
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+ //Custom data model
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+ const customData = {
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+ displayNavigation: true, // Set to false to hide navigation scale
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+ displaySequence: true, // Set to false to hide sequence track
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+ sequence: 'MPNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE', //Protein sequence
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+ length: 138, // Length of the sequence
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+ offset: 1, // Offset navigation scale start. Example offset:10 will display the navigation start from 10 instead of default 1.
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+ tracks: [ // Array of track objects (PDBe implementation extends core ProtVista track component. Refer - https://github.com/ebi-webcomponents/nightingale/tree/master/packages/protvista-track#data-array for all the supported track properties )
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+ {
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+ label: "Domains", // Track label
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+ labelType: "text", // Supported values 'text' and 'html'
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+ data: [
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+ {
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+ accession: "d1", // Some unique id
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+ type: "UniProt range", // Displayed in tooltip title
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+ label: "Domain 1", // Expected values 'text' and 'html'
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+ labelTooltip: "Residues mapped to domain 1", // Label tooltip content. Support text and HTML mark-up
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+ locations: [ // Array of sub-tracks
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+ {
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+ fragments : [ // Array of sub-track fragments
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+ {
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+ start: 1, // Track start value
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+ end: 56, // Track end value
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+ tooltipContent: "Type: domain 1<br>Range: XYZ1 - XYZ56", // track tooltip content. Support text and HTML mark-up
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+ color: "rgb(135,158,247)" // track (fragment) colour, supported rgb and hex code value
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+ },
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+ {
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+ start: 70,
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+ end: 130,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130",
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+ color: "rgb(160,174,232)"
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+ }
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+ ]
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+ }
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+ ]
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+ },
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+ {
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+ accession: "d2",
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+ type: "UniProt range",
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+ label: "<div><i class='icon icon-generic' data-icon=';' style='color: #000;'></i> <a href='resource.xyz'>Domain 2</a></div>", //HTML strcutured label with font-icons. You can add any HTML markup.
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+ labelTooltip: "<strong>Domain Compound</strong><br><img src='https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/REA_200.svg'>", // labelTooltip HTML mark-up example displaying compound image in the tooltip.
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+ locations: [
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+ {
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+ fragments : [
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+ {
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+ start: 1,
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+ end: 20,
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+ tooltipContent: "<strong>Type: domain 2</strong><br>Range: XY1 - XYZ20<br><a href='resource.xyz' style='color:blue'>view details</a>", // tooltipContent HTML mark-up example
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+ color: "rgb(107,119,39)"
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+ },
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+ {
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+ start: 22,
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+ end: 137,
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+ tooltipContent: "Type: domain 2<br>Range: XYZ22 - XYZ137",
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+ color: "rgb(90,102,23)"
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+ }
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+ ]
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+ }
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+ ]
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+ }
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+ ]
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+
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+ },
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+ {
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+ label: "Annotations",
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+ labelType: "text",
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+ labelColor: "rgb(128,128,128)", // Set labelColor to change label background colour
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+ data: [
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+ {
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+ accession: "a1",
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+ type: "UniProt range",
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+ label: "Annotations 1",
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+ labelType: "text",
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+ labelTooltip: "Residues mapped to annotations 1",
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+ labelColor: "rgb(211,211,211)",
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+ color: "rgb(255,99,163)",
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+ locations: [
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+ {
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+ fragments : [
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+ {
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+ start: 1,
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+ end: 56,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ1 - XYZ56"
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+ },
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+ {
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+ start: 70,
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+ end: 130,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130"
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+ }
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+ ]
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+ }
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+ ]
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+ }
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+ ]
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+
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+ },
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+ {
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+ label: "Annotation shapes",
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+ data: [
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+ {
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+ accession: "s1",
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+ type: "UniProt range",
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+ label: "Circle",
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+ color: "rgb(249,166,2)",
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+ shape: 'circle', // supported shapes rectangle|bridge|diamond|chevron|catFace|triangle|wave|hexagon|pentagon|circle|arrow|doubleBar,
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+ locations: [
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+ {
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+ fragments : [
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+ {
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+ start: 5,
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+ end: 5,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ1 - XYZ56",
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+ },
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+ {
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+ start: 9,
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+ end: 9,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130"
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+ }
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+ ]
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+ }
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+ ]
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+ },
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+ {
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+ accession: "s2",
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+ type: "UniProt range",
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+ label: "Diamond",
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+ shape: 'diamond',
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+ color: "rgb(255,99,163)", // Default colour value for all fragments in this track
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+ locations: [
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+ {
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+ fragments : [
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+ {
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+ start: 5,
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+ end: 5,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ1 - XYZ56"
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+ },
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+ {
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+ start: 9,
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+ end: 9,
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+ color: "rgb(0,128,129)", // Set colour here for individual shape fragment. This will override the track default colour.
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130"
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+ },
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+ {
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+ start: 20,
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+ end: 20,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130"
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+ },
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+ {
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+ start: 22,
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+ end: 22,
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+ tooltipContent: "Type: domain 1<br>Range: XYZ70 - XYZ130"
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+ }
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+ ]
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+ }
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+ ]
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+ }
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+ ]
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+
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+ }
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+ ],
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+ sequenceConservation: seqConservationData, // Set this property to display your own sequence conservation data. Refer comments at the top for data structure.
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+ variants: variationData, // Set this property to display your own variation data. Refer comments at the top for data structure.
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+ legends: {
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+ alignment: 'right', // expected values 'left', 'right' or 'center'
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+ data: { // Legend Row, key is used as the row label
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+ "Domains": [ // legends for Domains row
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+ {
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+ color: ["rgb(135,158,247)", "rgb(160,174,232)"], // legend color, supported rgb and hex code value
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+ text: "Domains 1" // legend text
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+ },
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+ {
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+ color: ["rgb(107,119,39)", "rgb(90,102,23)"],
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+ text: "Domains 2"
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+ }
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+ ],
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+ "Annotations": [ // legends for Annotation row row
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+ {
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+ color: ["rgb(255,99,163)"],
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+ text: "Custom Annotations"
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+ }
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+ ]
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+ }
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+ }
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+ };
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+
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+ // Assign custom data object to instance viewerdata property
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+ pvInstance.viewerdata = customData;
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+
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+ })();
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+
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+ });
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+ </script>
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+
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+
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+ </body>
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+
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  </html>