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
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<html lang="en">
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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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<title>Mol* Plugin Wrapper</title>
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<style>
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}
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#app {
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position: absolute;
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left: 160px;
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width: 600px;
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height: 600px;
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border: 1px solid #ccc;
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}
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#controls {
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width: 130px;
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left: 10px;
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}
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#controls > button {
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text-align: left;
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}
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#controls > hr {
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margin: 5px 0;
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}
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#controls > input, #controls > select {
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width: 100%;
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display: block;
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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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<script type="text/javascript" src="./index.js"></script>
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</head>
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<body>
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<div id='controls'>
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<h3>Source</h3>
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<input type='text' id='url' placeholder='url' />
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<input type='text' id='assemblyId' placeholder='assembly id' />
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<select id='format'>
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<option value='mmcif' selected>mmCIF</option>
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<option value='pdb'>PDB</option>
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</select>
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</div>
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<div id="app"></div>
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<script>
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function $(id) { return document.getElementById(id); }
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var pdbId = '1grm', assemblyId= '1';
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var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
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var format = 'mmcif';
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$('url').value = url;
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$('url').onchange = function (e) { url = e.target.value; }
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$('assemblyId').value = assemblyId;
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$('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
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$('format').value = format;
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$('format').onchange = function (e) { format = e.target.value; }
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BasicMolStarWrapper.init('app' /** or document.getElementById('app') */).then(() => {
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BasicMolStarWrapper.setBackground(0xffffff);
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});
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addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
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addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
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addSeparator();
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addHeader('Camera');
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addControl('Toggle Spin', () => BasicMolStarWrapper.toggleSpin());
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addSeparator();
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addHeader('Animation');
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// adjust this number to make the animation faster or slower
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// requires to "restart" the animation if changed
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BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
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addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
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addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());
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addControl('Play Palindrome', () => BasicMolStarWrapper.animate.modelIndex.palindrome());
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addControl('Play Loop', () => BasicMolStarWrapper.animate.modelIndex.loop());
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addControl('Stop', () => BasicMolStarWrapper.animate.modelIndex.stop());
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addHeader('Misc');
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addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
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addControl('Apply Custom Theme', () => BasicMolStarWrapper.coloring.applyCustomTheme());
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addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
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addHeader('Interactivity');
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addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
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addControl('Clear Highlight', () => BasicMolStarWrapper.interactivity.clearHighlight());
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addHeader('Tests');
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addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
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addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
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addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
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addControl('Show Toasts', () => BasicMolStarWrapper.tests.showToasts());
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addControl('Hide Toasts', () => BasicMolStarWrapper.tests.hideToasts());
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////////////////////////////////////////////////////////
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function addControl(label, action) {
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$('controls').appendChild(btn);
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function addSeparator() {
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$('controls').appendChild(hr);
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}
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function addHeader(header) {
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$('controls').appendChild(h);
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}
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</script>
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</body>
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<!DOCTYPE html>
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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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<title>Mol* Plugin Wrapper</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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#app {
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position: absolute;
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left: 160px;
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top: 100px;
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width: 600px;
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height: 600px;
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border: 1px solid #ccc;
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}
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#controls {
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position: absolute;
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width: 130px;
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left: 10px;
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}
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}
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#controls > input, #controls > select {
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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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<input type='text' id='url' placeholder='url' />
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<input type='text' id='assemblyId' placeholder='assembly id' />
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<option value='mmcif' selected>mmCIF</option>
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</div>
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var url = 'https://www.ebi.ac.uk/pdbe/static/entry/' + pdbId + '_updated.cif';
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$('url').value = url;
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$('url').onchange = function (e) { url = e.target.value; }
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$('assemblyId').value = assemblyId;
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$('assemblyId').onchange = function (e) { assemblyId = e.target.value; }
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$('format').value = format;
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$('format').onchange = function (e) { format = e.target.value; }
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BasicMolStarWrapper.init('app' /** or document.getElementById('app') */).then(() => {
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BasicMolStarWrapper.setBackground(0xffffff);
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});
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addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
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addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));
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addSeparator();
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addHeader('Camera');
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addControl('Toggle Spin', () => BasicMolStarWrapper.toggleSpin());
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addSeparator();
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addHeader('Animation');
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// adjust this number to make the animation faster or slower
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// requires to "restart" the animation if changed
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BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
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addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
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addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());
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addControl('Play Palindrome', () => BasicMolStarWrapper.animate.modelIndex.palindrome());
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addControl('Play Loop', () => BasicMolStarWrapper.animate.modelIndex.loop());
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addControl('Stop', () => BasicMolStarWrapper.animate.modelIndex.stop());
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addHeader('Misc');
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addControl('Apply Stripes', () => BasicMolStarWrapper.coloring.applyStripes());
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addControl('Apply Custom Theme', () => BasicMolStarWrapper.coloring.applyCustomTheme());
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addControl('Default Coloring', () => BasicMolStarWrapper.coloring.applyDefault());
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addHeader('Interactivity');
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addControl('Highlight seq_id=7', () => BasicMolStarWrapper.interactivity.highlightOn());
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addControl('Clear Highlight', () => BasicMolStarWrapper.interactivity.clearHighlight());
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addHeader('Tests');
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addControl('Static Superposition', () => BasicMolStarWrapper.tests.staticSuperposition());
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addControl('Dynamic Superposition', () => BasicMolStarWrapper.tests.dynamicSuperposition());
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addControl('Validation Tooltip', () => BasicMolStarWrapper.tests.toggleValidationTooltip());
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addControl('Show Toasts', () => BasicMolStarWrapper.tests.showToasts());
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addControl('Hide Toasts', () => BasicMolStarWrapper.tests.hideToasts());
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////////////////////////////////////////////////////////
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function addControl(label, action) {
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var btn = document.createElement('button');
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btn.onclick = action;
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btn.innerText = label;
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$('controls').appendChild(btn);
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}
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function addSeparator() {
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var hr = document.createElement('hr');
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$('controls').appendChild(hr);
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}
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function addHeader(header) {
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var h = document.createElement('h3');
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h.innerText = header;
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$('controls').appendChild(h);
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}
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</script>
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</body>
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@@ -1,89 +1,89 @@
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<!DOCTYPE html>
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<html lang="en">
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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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<title>Mol* Lighting Demo</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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#app {
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position: absolute;
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width: 100%;
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height: 100%;
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}
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#controls {
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position: absolute;
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width: 150px;
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bottom: 100px;
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right: 50px;
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z-index: 10;
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font-family: sans-serif;
|
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font-size: smaller;
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}
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#controls > button {
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display: block;
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width: 100%;
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text-align: left;
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margin: 5px 0px;
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|
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}
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#controls > input, #controls > select {
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width: 100%;
|
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display: block;
|
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|
-
}
|
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|
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</style>
|
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41
|
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<link rel="stylesheet" type="text/css" href="molstar.css" />
|
|
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|
-
<script type="text/javascript" src="./index.js"></script>
|
|
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|
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</head>
|
|
44
|
-
<body>
|
|
45
|
-
<div id='controls'></div>
|
|
46
|
-
<div id="app"></div>
|
|
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|
-
<script>
|
|
48
|
-
LightingDemo.init('app').then(() => {
|
|
49
|
-
LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3);
|
|
50
|
-
});
|
|
51
|
-
|
|
52
|
-
addHeader('Example PDB IDs');
|
|
53
|
-
addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
|
|
54
|
-
addControl('5FJ5', () => LightingDemo.load({ url: 'https://models.rcsb.org/5FJ5.bcif', assemblyId: '1' }, 8, 1.8));
|
|
55
|
-
addControl('1UPN', () => LightingDemo.load({ url: 'https://models.rcsb.org/1UPN.bcif', assemblyId: '1' }, 7, 1.6));
|
|
56
|
-
addControl('1RB8', () => LightingDemo.load({ url: 'https://models.rcsb.org/1RB8.bcif', assemblyId: '1' }, 6, 1.3));
|
|
57
|
-
|
|
58
|
-
addSeparator()
|
|
59
|
-
|
|
60
|
-
addHeader('Lighting Presets');
|
|
61
|
-
addControl('Illustrative', () => LightingDemo.setPreset('illustrative'));
|
|
62
|
-
addControl('Standard', () => LightingDemo.setPreset('standard'));
|
|
63
|
-
addControl('Ambient Occlusion', () => LightingDemo.setPreset('occlusion'));
|
|
64
|
-
|
|
65
|
-
////////////////////////////////////////////////////////
|
|
66
|
-
|
|
67
|
-
function $(id) { return document.getElementById(id); }
|
|
68
|
-
|
|
69
|
-
function addControl(label, action) {
|
|
70
|
-
var btn = document.createElement('button');
|
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|
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btn.onclick = action;
|
|
72
|
-
btn.innerText = label;
|
|
73
|
-
$('controls').appendChild(btn);
|
|
74
|
-
}
|
|
75
|
-
|
|
76
|
-
function addSeparator() {
|
|
77
|
-
var hr = document.createElement('br');
|
|
78
|
-
$('controls').appendChild(hr);
|
|
79
|
-
}
|
|
80
|
-
|
|
81
|
-
function addHeader(header) {
|
|
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|
-
var h = document.createElement('h3');
|
|
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|
-
h.innerText = header;
|
|
84
|
-
$('controls').appendChild(h);
|
|
85
|
-
}
|
|
86
|
-
</script>
|
|
87
|
-
<!-- __MOLSTAR_ANALYTICS__ -->
|
|
88
|
-
</body>
|
|
1
|
+
<!DOCTYPE html>
|
|
2
|
+
<html lang="en">
|
|
3
|
+
<head>
|
|
4
|
+
<meta charset="utf-8" />
|
|
5
|
+
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
|
|
6
|
+
<title>Mol* Lighting Demo</title>
|
|
7
|
+
<style>
|
|
8
|
+
* {
|
|
9
|
+
margin: 0;
|
|
10
|
+
padding: 0;
|
|
11
|
+
box-sizing: border-box;
|
|
12
|
+
}
|
|
13
|
+
#app {
|
|
14
|
+
position: absolute;
|
|
15
|
+
width: 100%;
|
|
16
|
+
height: 100%;
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
#controls {
|
|
20
|
+
position: absolute;
|
|
21
|
+
width: 150px;
|
|
22
|
+
bottom: 100px;
|
|
23
|
+
right: 50px;
|
|
24
|
+
z-index: 10;
|
|
25
|
+
font-family: sans-serif;
|
|
26
|
+
font-size: smaller;
|
|
27
|
+
}
|
|
28
|
+
|
|
29
|
+
#controls > button {
|
|
30
|
+
display: block;
|
|
31
|
+
width: 100%;
|
|
32
|
+
text-align: left;
|
|
33
|
+
margin: 5px 0px;
|
|
34
|
+
}
|
|
35
|
+
|
|
36
|
+
#controls > input, #controls > select {
|
|
37
|
+
width: 100%;
|
|
38
|
+
display: block;
|
|
39
|
+
}
|
|
40
|
+
</style>
|
|
41
|
+
<link rel="stylesheet" type="text/css" href="molstar.css" />
|
|
42
|
+
<script type="text/javascript" src="./index.js"></script>
|
|
43
|
+
</head>
|
|
44
|
+
<body>
|
|
45
|
+
<div id='controls'></div>
|
|
46
|
+
<div id="app"></div>
|
|
47
|
+
<script>
|
|
48
|
+
LightingDemo.init('app').then(() => {
|
|
49
|
+
LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3);
|
|
50
|
+
});
|
|
51
|
+
|
|
52
|
+
addHeader('Example PDB IDs');
|
|
53
|
+
addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
|
|
54
|
+
addControl('5FJ5', () => LightingDemo.load({ url: 'https://models.rcsb.org/5FJ5.bcif', assemblyId: '1' }, 8, 1.8));
|
|
55
|
+
addControl('1UPN', () => LightingDemo.load({ url: 'https://models.rcsb.org/1UPN.bcif', assemblyId: '1' }, 7, 1.6));
|
|
56
|
+
addControl('1RB8', () => LightingDemo.load({ url: 'https://models.rcsb.org/1RB8.bcif', assemblyId: '1' }, 6, 1.3));
|
|
57
|
+
|
|
58
|
+
addSeparator()
|
|
59
|
+
|
|
60
|
+
addHeader('Lighting Presets');
|
|
61
|
+
addControl('Illustrative', () => LightingDemo.setPreset('illustrative'));
|
|
62
|
+
addControl('Standard', () => LightingDemo.setPreset('standard'));
|
|
63
|
+
addControl('Ambient Occlusion', () => LightingDemo.setPreset('occlusion'));
|
|
64
|
+
|
|
65
|
+
////////////////////////////////////////////////////////
|
|
66
|
+
|
|
67
|
+
function $(id) { return document.getElementById(id); }
|
|
68
|
+
|
|
69
|
+
function addControl(label, action) {
|
|
70
|
+
var btn = document.createElement('button');
|
|
71
|
+
btn.onclick = action;
|
|
72
|
+
btn.innerText = label;
|
|
73
|
+
$('controls').appendChild(btn);
|
|
74
|
+
}
|
|
75
|
+
|
|
76
|
+
function addSeparator() {
|
|
77
|
+
var hr = document.createElement('br');
|
|
78
|
+
$('controls').appendChild(hr);
|
|
79
|
+
}
|
|
80
|
+
|
|
81
|
+
function addHeader(header) {
|
|
82
|
+
var h = document.createElement('h3');
|
|
83
|
+
h.innerText = header;
|
|
84
|
+
$('controls').appendChild(h);
|
|
85
|
+
}
|
|
86
|
+
</script>
|
|
87
|
+
<!-- __MOLSTAR_ANALYTICS__ -->
|
|
88
|
+
</body>
|
|
89
89
|
</html>
|