molstar-volseg
v0.0.15
Published
MolStar extension for visualizing volumetric and segmentation data
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Mol* Volumes & Segmentations
Mol* Volumes & Segmentations 2.0 (Mol* VS 2.0) is a next iteration of web application designed for real-time visualization of large-scale volumetric, segmentation, and annotation data.
Running Mol* viewer with Mol* Volumes & Segmentations extension
- Create new folder, e.g.:
mkdir molstar-volseg-viewer- Change directory to it, e.g.:
cd molstar-volseg-viewer- Initialize new npm package:
npm init -y- Install Mol* and Mol* Volumes & Segmentations extension npm packages:
npm install molstar
npm install molstar-volseg- Create
index.htmlfile inmolstar-volseg-viewerwith the following content:
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<link rel="icon" href="./favicon.ico" type="image/x-icon">
<title>Mol* Viewer</title>
<style>
* {
margin: 0;
padding: 0;
box-sizing: border-box;
}
html, body {
width: 100%;
height: 100%;
overflow: hidden;
}
hr {
margin: 10px;
}
h1, h2, h3, h4, h5 {
margin-top: 5px;
margin-bottom: 3px;
}
button {
padding: 2px;
}
#app {
position: absolute;
left: 100px;
top: 100px;
width: 800px;
height: 600px;
}
</style>
<link rel="stylesheet" type="text/css" href="molstar.css" />
</head>
<body>
<div id="app"></div>
<script type="module">
import * as molstar from './molstar.mjs';
console.log('imported molstar.mjs');
console.log(molstar);
function getParam(name, regex) {
var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
}
var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
if (debugMode) molstar.setDebugMode(debugMode);
var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
if (timingMode) molstar.setTimingMode(timingMode);
var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
var pixelScale = getParam('pixel-scale', '[^&]+').trim();
var pickScale = getParam('pick-scale', '[^&]+').trim();
var pickPadding = getParam('pick-padding', '[^&]+').trim();
var transparency = getParam('transparency', '[^&]+').trim().toLowerCase();
var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
// console.log('Available extensions: ', Object.keys(molstar.ExtensionMap));
molstar.Viewer.create('app', {
disabledExtensions: [], // anything from Object.keys(molstar.ExtensionMap)
layoutShowControls: !hideControls,
viewportShowExpand: false,
collapseLeftPanel: collapseLeftPanel,
pdbProvider: pdbProvider || 'pdbe',
emdbProvider: emdbProvider || 'pdbe',
volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
? 'https://maps.rcsb.org'
: 'https://www.ebi.ac.uk/pdbe/densities',
pixelScale: parseFloat(pixelScale) || 1,
pickScale: parseFloat(pickScale) || 0.25,
pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
transparency: transparency || undefined,
preferWebgl1: preferWebgl1,
allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
powerPreference: powerPreference || 'high-performance',
}).then(viewer => {
var snapshotId = getParam('snapshot-id', '[^&]+').trim();
if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
var structureUrl = getParam('structure-url', '[^&]+').trim();
var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
var mvsUrl = getParam('mvs-url', '[^&]+').trim();
var mvsData = getParam('mvs-data', '[^&]+').trim();
var mvsFormat = getParam('mvs-format', '[^&]+').trim() || 'mvsj';
if (mvsUrl && mvsData) console.error('Cannot specify mvs-url and mvs-data URL parameters at the same time. Ignoring both.');
else if (mvsUrl) viewer.loadMvsFromUrl(mvsUrl, mvsFormat);
else if (mvsData) viewer.loadMvsData(mvsData, mvsFormat);
var cvsxUrl = getParam('cvsx-url', '[^&]+').trim();
var cvsxFormat = getParam('cvsx-format', '[^&]+').trim() || 'cvsx';
if (cvsxUrl) viewer.loadCvsxFromUrl(cvsxUrl, cvsxFormat)
var pdb = getParam('pdb', '[^&]+').trim();
if (pdb) viewer.loadPdb(pdb);
var pdbDev = getParam('pdb-dev', '[^&]+').trim();
if (pdbDev) viewer.loadPdbDev(pdbDev);
var emdb = getParam('emdb', '[^&]+').trim();
if (emdb) viewer.loadEmdb(emdb);
var afdb = getParam('afdb', '[^&]+').trim();
if (afdb) viewer.loadAlphaFoldDb(afdb);
var modelArchive = getParam('model-archive', '[^&]+').trim();
if (modelArchive) viewer.loadModelArchive(modelArchive);
window.addEventListener('unload', () => {
// to aid GC
viewer.dispose();
});
});
</script>
<!-- __MOLSTAR_ANALYTICS__ -->
</body>
</html>- Copy
molstar.mjsandmolstar.cssfiles frombuildfolder ofmolstar-volsegNPM package (node_modules\molstar-volseg\build) tomolstar-volseg-viewer:
cp node_modules/molstar-volseg/build/molstar.css .
cp node_modules/molstar-volseg/build/molstar.mjs .- Install
http-serverNPM module globally:
npm install http-server -g- Serve the
index.htmlwebpage usinghttp-server. Frommolstar-volseg-viewerdirectory run:
http-serverIt will serve the webpage with Mol* Viewer with Mol* Volumes & Segmentations extension at http://127.0.0.1:8080 by default.