npm - molstar - Versions diffs - 4.3.0 → 4.4.1 - Mend

molstar 4.3.0 → 4.4.1

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.

Files changed (1384) hide show

package/lib/apps/viewer/app.js CHANGED Viewed

@@ -3,6 +3,7 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Neli Fonseca <neli@ebi.ac.uk>
  */
 import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { Backgrounds } from '../../extensions/backgrounds';
@@ -41,6 +42,7 @@ import { PluginSpec } from '../../mol-plugin/spec';
 import { StateObjectRef } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import '../../mol-util/polyfill';
 import { ObjectKeys } from '../../mol-util/type-helpers';
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
@@ -385,6 +387,32 @@ export class Viewer {
             await repr.commit();
         });
     }
+    loadFullResolutionEMDBMap(emdbId, options) {
+        const plugin = this.plugin;
+        const numericId = parseInt(emdbId.toUpperCase().replace('EMD-', ''));
+        const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;
+        return plugin.dataTransaction(async () => {
+            var _a, _b, _c;
+            const data = await plugin.build().toRoot()
+                .apply(StateTransforms.Data.Download, { url, isBinary: true, label: emdbId }, { state: { isGhost: true } })
+                .apply(StateTransforms.Data.DeflateData)
+                .commit();
+            const parsed = await plugin.dataFormats.get('ccp4').parse(plugin, data, { entryId: emdbId });
+            const firstVolume = (parsed.volume || parsed.volumes[0]);
+            if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
+                throw new Error('Failed to parse any volume.');
+            const volume = (_b = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : parsed.volume;
+            await plugin.build()
+                .to(volume)
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data, {
+                type: 'isosurface',
+                typeParams: { alpha: 1, isoValue: options.isoValue },
+                color: 'uniform',
+                colorParams: { value: (_c = options.color) !== null && _c !== void 0 ? _c : Color(0x33BB33) }
+            }))
+                .commit();
+        });
+    }
     /**
      * @example
      *  viewer.loadTrajectory({

package/lib/apps/viewer/embedded.html CHANGED Viewed

@@ -1,53 +1,53 @@
-<!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>Embedded Mol* Viewer</title>
-        <style>
-            #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="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            molstar.Viewer.create('app', {
-                layoutIsExpanded: true,
-                layoutShowControls: false,
-                layoutShowRemoteState: false,
-                layoutShowSequence: true,
-                layoutShowLog: false,
-                layoutShowLeftPanel: true,
-                viewportShowExpand: true,
-                viewportShowSelectionMode: false,
-                viewportShowAnimation: false,
-                pdbProvider: 'rcsb',
-                emdbProvider: 'rcsb',
-            }).then(viewer => {
-                viewer.loadPdb('7bv2');
-                viewer.loadEmdb('EMD-30210', { detail: 6 });
-                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
-                //     representationParams: {
-                //         theme: {
-                //             globalName: 'uniform',
-                //             globalColorParams: { value: 0xff0000 }
-                //         }
-                //     },
-                //     label: 'my structure'
-                // });
-            });
-        </script>
-    </body>
+<!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>Embedded Mol* Viewer</title>
+        <style>
+            #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="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
+                //     representationParams: {
+                //         theme: {
+                //             globalName: 'uniform',
+                //             globalColorParams: { value: 0xff0000 }
+                //         }
+                //     },
+                //     label: 'my structure'
+                // });
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/index.html CHANGED Viewed

@@ -1,130 +1,130 @@
-<!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="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            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 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>
+<!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="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            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 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>

package/lib/cli/chem-comp-dict/create-ions.js CHANGED Viewed

@@ -25,15 +25,15 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    const output = `/**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/chem-comp-dict/create-ions cli
- */
-export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+    const output = `/**
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/chem-comp-dict/create-ions cli
+ */
+export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
     writeFile(filePath, output);
 }

package/lib/cli/chem-comp-dict/create-saccharides.js CHANGED Viewed

@@ -26,15 +26,15 @@ function extractSaccharideNames(ccd) {
     return saccharideNames;
 }
 function writeSaccharideNamesFile(filePath, ionNames) {
-    const output = `/**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/cli/chem-comp-dict/create-saccharides
- */
-export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
 `;
     writeFile(filePath, output);
 }

package/lib/cli/cifschema/util/generate.js CHANGED Viewed

@@ -6,21 +6,21 @@
 import { indentString } from '../../../mol-util/string';
 import { FieldPath } from '../../../mol-io/reader/cif/schema';
 function header(name, info, moldataImportPath) {
-    return `/**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated '${name}' schema file. ${info}
- *
- * @author molstar/ciftools package
- */
-import { Database, Column } from '${moldataImportPath}/db';
+    return `/**
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated '${name}' schema file. ${info}
+ *
+ * @author molstar/ciftools package
+ */
+import { Database, Column } from '${moldataImportPath}/db';
 import Schema = Column.Schema;`;
 }
 function footer(name) {
-    return `
-export type ${name}_Schema = typeof ${name}_Schema;
+    return `
+export type ${name}_Schema = typeof ${name}_Schema;
 export interface ${name}_Database extends Database<${name}_Schema> {};`;
 }
 function getTypeShorthands(schema, fields) {

package/lib/cli/lipid-params/index.js CHANGED Viewed

@@ -41,15 +41,15 @@ async function run(out) {
     }
     const lipidNames = JSON.stringify(lipids.array);
     if (out) {
-        const output = `/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
+        const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+ *
+ * @author molstar/lipid-params cli
+ */
+export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
 `;
         fs.writeFileSync(out, output);
     }

package/lib/commonjs/apps/docking-viewer/viewport.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/apps/docking-viewer/viewport.js CHANGED Viewed

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ViewportComponent = exports.ShowButtons = exports.IllustrativePreset = exports.StructurePreset = void 0;
 const jsx_runtime_1 = require("react/jsx-runtime");
 /**
- * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -45,6 +45,7 @@ function occlusionStyle(plugin) {
                 ...plugin.canvas3d.props.postprocessing,
                 occlusion: { name: 'on', params: {
                         blurKernelSize: 15,
+                        blurDepthBias: 0.5,
                         multiScale: { name: 'off', params: {} },
                         radius: 5,
                         bias: 0.8,

package/lib/commonjs/apps/mesoscale-explorer/app.d.ts CHANGED Viewed

@@ -24,12 +24,13 @@ export type MesoscaleExplorerState = {
     examples?: ExampleEntry[];
     graphicsMode: GraphicsMode;
     stateRef?: string;
+    driver?: any;
     stateCache: {
         [k: string]: any;
     };
 };
 declare const DefaultMesoscaleExplorerOptions: {
-    customFormats: [string, DataFormatProvider<any, any, any>][];
+    customFormats: [string, DataFormatProvider][];
     extensions: ("mp4-export" | "backgrounds")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
@@ -60,6 +61,7 @@ declare const DefaultMesoscaleExplorerOptions: {
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
     saccharideCompIdMapType: SaccharideCompIdMapType;
     graphicsMode: GraphicsMode;
+    driver: undefined;
 };
 type MesoscaleExplorerOptions = typeof DefaultMesoscaleExplorerOptions;
 export declare class MesoscaleExplorer {

package/lib/commonjs/apps/mesoscale-explorer/app.js CHANGED Viewed

@@ -27,6 +27,7 @@ const assets_1 = require("../../mol-util/assets");
 const camera_spin_1 = require("../../mol-plugin-state/animation/built-in/camera-spin");
 const camera_rock_1 = require("../../mol-plugin-state/animation/built-in/camera-rock");
 const state_snapshots_1 = require("../../mol-plugin-state/animation/built-in/state-snapshots");
+const entities_1 = require("./ui/entities");
 var version_1 = require("../../mol-plugin/version");
 Object.defineProperty(exports, "version", { enumerable: true, get: function () { return version_1.PLUGIN_VERSION; } });
 var debug_1 = require("../../mol-util/debug");
@@ -70,7 +71,8 @@ const DefaultMesoscaleExplorerOptions = {
     pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default',
-    graphicsMode: 'quality'
+    graphicsMode: 'quality',
+    driver: undefined
 };
 class MesoscaleExplorer {
     constructor(plugin) {
@@ -142,6 +144,9 @@ class MesoscaleExplorer {
                     right: panels_1.RightPanel,
                 },
                 remoteState: 'none',
+                viewport: {
+                    snapshotDescription: entities_1.MesoViewportSnapshotDescription,
+                }
             },
             config: [
                 [config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
@@ -179,6 +184,11 @@ class MesoscaleExplorer {
                 let examples = undefined;
                 try {
                     examples = await plugin.fetch({ url: './examples/list.json', type: 'json' }).run();
+                    // extend the array with file tour.json if it exists
+                    const tour = await plugin.fetch({ url: './examples/tour.json', type: 'json' }).run();
+                    if (tour) {
+                        examples = examples === null || examples === void 0 ? void 0 : examples.concat(tour);
+                    }
                 }
                 catch (e) {
                     console.log(e);
@@ -186,6 +196,7 @@ class MesoscaleExplorer {
                 plugin.customState = {
                     examples,
                     graphicsMode: o.graphicsMode,
+                    driver: o.driver,
                     stateCache: {},
                 };
                 await state_1.MesoscaleState.init(plugin);