molstar 3.1.0 → 3.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/LICENSE +20 -20
- package/README.md +194 -194
- package/build/viewer/embedded.html +43 -43
- package/build/viewer/index.html +106 -106
- package/build/viewer/molstar.js +1 -1
- package/lib/apps/docking-viewer/index.html +36 -36
- package/lib/apps/viewer/embedded.html +43 -43
- package/lib/apps/viewer/index.html +106 -106
- package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts +0 -1
- package/lib/commonjs/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.d.ts +22 -0
- package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js +22 -0
- package/lib/commonjs/mol-model/structure/export/categories/atom_site.js +68 -1
- package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts +21 -0
- package/lib/commonjs/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js} +40 -20
- package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts +5 -0
- package/lib/commonjs/mol-model-formats/structure/common/property.d.ts +5 -2
- package/lib/commonjs/mol-model-formats/structure/common/property.js +20 -8
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.d.ts +1 -0
- package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js +2 -1
- package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +7 -5
- package/lib/commonjs/mol-model-props/sequence/{best-database-mapping.js → sifts-mapping.js} +29 -26
- package/lib/{mol-model-props/sequence/themes/best-database-mapping.d.ts → commonjs/mol-model-props/sequence/themes/sifts-mapping.d.ts} +5 -5
- package/lib/commonjs/mol-model-props/sequence/themes/{best-database-mapping.js → sifts-mapping.js} +22 -22
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +1 -1
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.js → sifts-mapping.js} +11 -11
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.d.ts +1 -1
- package/lib/commonjs/mol-plugin/behavior/dynamic/custom-props.js +2 -2
- package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- package/lib/commonjs/mol-plugin-ui/structure/superposition.d.ts +4 -1
- package/lib/commonjs/mol-plugin-ui/structure/superposition.js +66 -30
- package/lib/commonjs/mol-script/language/builder.d.ts +1 -0
- package/lib/examples/alpha-orbitals/index.html +61 -61
- package/lib/examples/basic-wrapper/index.html +137 -137
- package/lib/examples/lighting/index.html +88 -88
- package/lib/examples/proteopedia-wrapper/index.html +236 -236
- package/lib/mol-geo/geometry/cylinders/cylinders.d.ts +2 -2
- package/lib/mol-geo/geometry/lines/lines.d.ts +0 -1
- package/lib/mol-geo/geometry/points/points.d.ts +1 -1
- package/lib/mol-io/reader/cif/schema/mmcif.d.ts +22 -0
- package/lib/mol-io/reader/cif/schema/mmcif.js +22 -0
- package/lib/mol-model/structure/export/categories/atom_site.js +68 -1
- package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.d.ts +21 -0
- package/lib/mol-model/structure/structure/util/{superposition-db-mapping.js → superposition-sifts-mapping.js} +38 -18
- package/lib/mol-model-formats/structure/basic/schema.d.ts +5 -0
- package/lib/mol-model-formats/structure/common/property.d.ts +5 -2
- package/lib/mol-model-formats/structure/common/property.js +20 -8
- package/lib/mol-model-formats/structure/property/bonds/index-pair.d.ts +1 -0
- package/lib/mol-model-formats/structure/property/bonds/index-pair.js +2 -1
- package/lib/mol-model-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +7 -5
- package/lib/mol-model-props/sequence/{best-database-mapping.js → sifts-mapping.js} +28 -25
- package/lib/{commonjs/mol-model-props/sequence/themes/best-database-mapping.d.ts → mol-model-props/sequence/themes/sifts-mapping.d.ts} +5 -5
- package/lib/mol-model-props/sequence/themes/{best-database-mapping.js → sifts-mapping.js} +19 -19
- package/lib/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.d.ts → sifts-mapping.d.ts} +1 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props/sequence/{best-database-mapping.js → sifts-mapping.js} +8 -8
- package/lib/mol-plugin/behavior/dynamic/custom-props.d.ts +1 -1
- package/lib/mol-plugin/behavior/dynamic/custom-props.js +1 -1
- package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts +2 -3
- package/lib/mol-plugin/version.js +2 -2
- package/lib/mol-plugin-ui/skin/base/base.scss +32 -32
- package/lib/mol-plugin-ui/skin/base/components/controls-base.scss +333 -333
- package/lib/mol-plugin-ui/skin/base/components/controls.scss +418 -418
- package/lib/mol-plugin-ui/skin/base/components/help.scss +27 -27
- package/lib/mol-plugin-ui/skin/base/components/line-graph.scss +67 -67
- package/lib/mol-plugin-ui/skin/base/components/log.scss +100 -100
- package/lib/mol-plugin-ui/skin/base/components/misc.scss +643 -643
- package/lib/mol-plugin-ui/skin/base/components/sequence.scss +125 -125
- package/lib/mol-plugin-ui/skin/base/components/slider.scss +165 -165
- package/lib/mol-plugin-ui/skin/base/components/tasks.scss +99 -99
- package/lib/mol-plugin-ui/skin/base/components/toast.scss +83 -83
- package/lib/mol-plugin-ui/skin/base/components/transformer.scss +163 -163
- package/lib/mol-plugin-ui/skin/base/components/viewport.scss +127 -127
- package/lib/mol-plugin-ui/skin/base/layout/common.scss +71 -71
- package/lib/mol-plugin-ui/skin/base/layout/controls-landscape.scss +89 -89
- package/lib/mol-plugin-ui/skin/base/layout/controls-outside.scss +98 -98
- package/lib/mol-plugin-ui/skin/base/layout/controls-portrait.scss +108 -108
- package/lib/mol-plugin-ui/skin/base/layout.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/logo.scss +12 -12
- package/lib/mol-plugin-ui/skin/base/normalize.scss +209 -209
- package/lib/mol-plugin-ui/skin/base/ui.scss +40 -40
- package/lib/mol-plugin-ui/skin/base/variables.scss +85 -85
- package/lib/mol-plugin-ui/skin/blue.scss +1 -1
- package/lib/mol-plugin-ui/skin/colors/blue.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/dark.scss +23 -23
- package/lib/mol-plugin-ui/skin/colors/light.scss +29 -29
- package/lib/mol-plugin-ui/skin/dark.scss +1 -1
- package/lib/mol-plugin-ui/skin/light.scss +1 -1
- package/lib/mol-plugin-ui/structure/superposition.d.ts +4 -1
- package/lib/mol-plugin-ui/structure/superposition.js +66 -30
- package/lib/mol-script/language/builder.d.ts +1 -0
- package/package.json +160 -160
- package/lib/commonjs/mol-model/structure/structure/util/superposition-db-mapping.d.ts +0 -13
- package/lib/mol-model/structure/structure/util/superposition-db-mapping.d.ts +0 -13
package/build/viewer/index.html
CHANGED
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<!DOCTYPE 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, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
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<link rel="icon" href="./favicon.ico" type="image/x-icon">
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<title>Mol* Viewer</title>
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margin: 0;
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html, body {
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overflow: hidden;
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}
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hr {
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margin: 10px;
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}
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h1, h2, h3, h4, h5 {
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margin-top: 5px;
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margin-bottom: 3px;
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}
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button {
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padding: 2px;
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}
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#app {
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width: 800px;
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}
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</style>
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<link rel="stylesheet" type="text/css" href="molstar.css" />
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</head>
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<body>
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<div id="app"></div>
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<script type="text/javascript" src="./molstar.js"></script>
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<script type="text/javascript">
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function getParam(name, regex) {
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var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
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return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
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}
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var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
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if (debugMode) molstar.setDebugMode(debugMode, debugMode);
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var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
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var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
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var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
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var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
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var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
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var pixelScale = getParam('pixel-scale', '[^&]+').trim();
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var pickScale = getParam('pick-scale', '[^&]+').trim();
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var pickPadding = getParam('pick-padding', '[^&]+').trim();
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var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
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var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
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molstar.Viewer.create('app', {
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layoutShowControls: !hideControls,
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viewportShowExpand: false,
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collapseLeftPanel: collapseLeftPanel,
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pdbProvider: pdbProvider || 'pdbe',
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emdbProvider: emdbProvider || 'pdbe',
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volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
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? 'https://maps.rcsb.org'
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: 'https://www.ebi.ac.uk/pdbe/densities',
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pixelScale: parseFloat(pixelScale) || 1,
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pickScale: parseFloat(pickScale) || 0.25,
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pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
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enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
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preferWebgl1: preferWebgl1,
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}).then(viewer => {
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var snapshotId = getParam('snapshot-id', '[^&]+').trim();
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if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
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var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
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var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
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if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
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var structureUrl = getParam('structure-url', '[^&]+').trim();
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var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
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var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
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if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
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var pdb = getParam('pdb', '[^&]+').trim();
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if (pdb) viewer.loadPdb(pdb);
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var pdbDev = getParam('pdb-dev', '[^&]+').trim();
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if (pdbDev) viewer.loadPdbDev(pdbDev);
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var emdb = getParam('emdb', '[^&]+').trim();
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if (emdb) viewer.loadEmdb(emdb);
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var afdb = getParam('afdb', '[^&]+').trim();
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if (afdb) viewer.loadAlphaFoldDb(afdb);
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var modelArchive = getParam('model-archive', '[^&]+').trim();
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if (modelArchive) viewer.loadModelArchive(modelArchive);
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});
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</script>
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<!-- __MOLSTAR_ANALYTICS__ -->
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</body>
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<!DOCTYPE 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, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
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<link rel="icon" href="./favicon.ico" type="image/x-icon">
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<title>Mol* Viewer</title>
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<style>
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* {
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margin: 0;
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padding: 0;
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box-sizing: border-box;
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}
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html, body {
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width: 100%;
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height: 100%;
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overflow: hidden;
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}
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hr {
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margin: 10px;
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}
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h1, h2, h3, h4, h5 {
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margin-top: 5px;
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margin-bottom: 3px;
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}
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button {
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padding: 2px;
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}
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#app {
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position: absolute;
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left: 100px;
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top: 100px;
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width: 800px;
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height: 600px;
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}
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</style>
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<link rel="stylesheet" type="text/css" href="molstar.css" />
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</head>
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<body>
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<div id="app"></div>
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<script type="text/javascript" src="./molstar.js"></script>
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<script type="text/javascript">
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function getParam(name, regex) {
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var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
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return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
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}
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var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
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if (debugMode) molstar.setDebugMode(debugMode, debugMode);
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var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
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var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
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var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
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var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
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var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
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var pixelScale = getParam('pixel-scale', '[^&]+').trim();
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var pickScale = getParam('pick-scale', '[^&]+').trim();
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var pickPadding = getParam('pick-padding', '[^&]+').trim();
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var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
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var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
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molstar.Viewer.create('app', {
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layoutShowControls: !hideControls,
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viewportShowExpand: false,
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collapseLeftPanel: collapseLeftPanel,
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pdbProvider: pdbProvider || 'pdbe',
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emdbProvider: emdbProvider || 'pdbe',
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volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
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? 'https://maps.rcsb.org'
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: 'https://www.ebi.ac.uk/pdbe/densities',
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pixelScale: parseFloat(pixelScale) || 1,
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pickScale: parseFloat(pickScale) || 0.25,
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pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
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enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
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preferWebgl1: preferWebgl1,
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}).then(viewer => {
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var snapshotId = getParam('snapshot-id', '[^&]+').trim();
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if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
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var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
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var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
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if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
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var structureUrl = getParam('structure-url', '[^&]+').trim();
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var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
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var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
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+
if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
|
|
88
|
+
|
|
89
|
+
var pdb = getParam('pdb', '[^&]+').trim();
|
|
90
|
+
if (pdb) viewer.loadPdb(pdb);
|
|
91
|
+
|
|
92
|
+
var pdbDev = getParam('pdb-dev', '[^&]+').trim();
|
|
93
|
+
if (pdbDev) viewer.loadPdbDev(pdbDev);
|
|
94
|
+
|
|
95
|
+
var emdb = getParam('emdb', '[^&]+').trim();
|
|
96
|
+
if (emdb) viewer.loadEmdb(emdb);
|
|
97
|
+
|
|
98
|
+
var afdb = getParam('afdb', '[^&]+').trim();
|
|
99
|
+
if (afdb) viewer.loadAlphaFoldDb(afdb);
|
|
100
|
+
|
|
101
|
+
var modelArchive = getParam('model-archive', '[^&]+').trim();
|
|
102
|
+
if (modelArchive) viewer.loadModelArchive(modelArchive);
|
|
103
|
+
});
|
|
104
|
+
</script>
|
|
105
|
+
<!-- __MOLSTAR_ANALYTICS__ -->
|
|
106
|
+
</body>
|
|
107
107
|
</html>
|